Project name: mutant4

Status: done

Started: 2024-06-16 06:41:01
Settings
Chain sequence(s) A: YEHQTSIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKSLPDYSCKVFTKVSPFMWGGASCYCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVKAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTDMSCEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISKSTALASAEFRVQQCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGGVGKQQAKDAEIQNSSLSQSYSRH
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:54)
[INFO]       Auto_mut: Residue number 87 from chain A and a score of 2.338 (phenylalanine)         
                       selected for automated muatation                                            (00:03:57)
[INFO]       Auto_mut: Residue number 88 from chain A and a score of 1.911 (methionine) selected   
                       for automated muatation                                                     (00:03:57)
[INFO]       Auto_mut: Residue number 89 from chain A and a score of 1.580 (tryptophan) selected   
                       for automated muatation                                                     (00:03:57)
[INFO]       Auto_mut: Residue number 257 from chain A and a score of 1.475 (phenylalanine)        
                       selected for automated muatation                                            (00:03:57)
[INFO]       Auto_mut: Residue number 388 from chain A and a score of 1.409 (valine) selected for  
                       automated muatation                                                         (00:03:57)
[INFO]       Auto_mut: Residue number 387 from chain A and a score of 1.368 (isoleucine) selected  
                       for automated muatation                                                     (00:03:57)
[INFO]       Auto_mut: Mutating residue number 88 from chain A (methionine) into glutamic acid     (00:03:57)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 87 from chain A (phenylalanine) into glutamic acid  (00:03:57)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 87 from chain A (phenylalanine) into aspartic acid  (00:03:57)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (phenylalanine) into arginine       (00:05:48)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (phenylalanine) into lysine         (00:05:49)
[INFO]       Auto_mut: Mutating residue number 88 from chain A (methionine) into lysine            (00:05:55)
[INFO]       Auto_mut: Mutating residue number 88 from chain A (methionine) into aspartic acid     (00:07:43)
[INFO]       Auto_mut: Mutating residue number 89 from chain A (tryptophan) into glutamic acid     (00:07:45)
[INFO]       Auto_mut: Mutating residue number 89 from chain A (tryptophan) into aspartic acid     (00:08:01)
[INFO]       Auto_mut: Mutating residue number 88 from chain A (methionine) into arginine          (00:09:34)
[INFO]       Auto_mut: Mutating residue number 89 from chain A (tryptophan) into lysine            (00:09:37)
[INFO]       Auto_mut: Mutating residue number 89 from chain A (tryptophan) into arginine          (00:09:56)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 257 from chain A (phenylalanine) into glutamic acid (00:11:33)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 257 from chain A (phenylalanine) into aspartic acid (00:11:33)
[INFO]       Auto_mut: Mutating residue number 388 from chain A (valine) into glutamic acid        (00:11:51)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (phenylalanine) into arginine      (00:13:26)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (phenylalanine) into lysine        (00:13:28)
[INFO]       Auto_mut: Mutating residue number 388 from chain A (valine) into lysine               (00:13:45)
[INFO]       Auto_mut: Mutating residue number 388 from chain A (valine) into aspartic acid        (00:15:18)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (isoleucine) into glutamic acid    (00:15:26)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (isoleucine) into aspartic acid    (00:15:46)
[INFO]       Auto_mut: Mutating residue number 388 from chain A (valine) into arginine             (00:17:10)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (isoleucine) into lysine           (00:17:18)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (isoleucine) into arginine         (00:17:37)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 0.3859 kcal/mol, Difference in average    
                       score from the base case: -0.0441                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (phenylalanine) into      
                       lysine: Energy difference: -0.0161 kcal/mol, Difference in average score    
                       from the base case: -0.0444                                                 (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 1.3670 kcal/mol, Difference in average    
                       score from the base case: -0.0431                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (phenylalanine) into      
                       arginine: Energy difference: -0.2424 kcal/mol, Difference in average score  
                       from the base case: -0.0446                                                 (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain A (methionine) into         
                       glutamic acid: Energy difference: -0.8077 kcal/mol, Difference in average   
                       score from the base case: -0.0232                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain A (methionine) into lysine: 
                       Energy difference: -1.0139 kcal/mol, Difference in average score from the   
                       base case: -0.0247                                                          (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain A (methionine) into         
                       aspartic acid: Energy difference: -0.3565 kcal/mol, Difference in average   
                       score from the base case: -0.0248                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain A (methionine) into         
                       arginine: Energy difference: -0.7653 kcal/mol, Difference in average score  
                       from the base case: -0.0299                                                 (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 89 from chain A (tryptophan) into         
                       glutamic acid: Energy difference: -0.0129 kcal/mol, Difference in average   
                       score from the base case: -0.0247                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 89 from chain A (tryptophan) into lysine: 
                       Energy difference: -0.0424 kcal/mol, Difference in average score from the   
                       base case: -0.0237                                                          (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 89 from chain A (tryptophan) into         
                       aspartic acid: Energy difference: 0.1215 kcal/mol, Difference in average    
                       score from the base case: -0.0245                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 89 from chain A (tryptophan) into         
                       arginine: Energy difference: 0.0309 kcal/mol, Difference in average score   
                       from the base case: -0.0295                                                 (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.8701 kcal/mol, Difference in average    
                       score from the base case: -0.0353                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.8356 kcal/mol, Difference in average score     
                       from the base case: -0.0342                                                 (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 2.4753 kcal/mol, Difference in average    
                       score from the base case: -0.0340                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.2516 kcal/mol, Difference in average score   
                       from the base case: -0.0418                                                 (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 388 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.3669 kcal/mol, Difference in average score from  
                       the base case: -0.0309                                                      (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 388 from chain A (valine) into lysine:    
                       Energy difference: -0.6089 kcal/mol, Difference in average score from the   
                       base case: -0.0304                                                          (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 388 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.8277 kcal/mol, Difference in average score from  
                       the base case: -0.0298                                                      (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 388 from chain A (valine) into arginine:  
                       Energy difference: -0.1940 kcal/mol, Difference in average score from the   
                       base case: -0.0304                                                          (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.0070 kcal/mol, Difference in average   
                       score from the base case: -0.0341                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.5554 kcal/mol, Difference in average score    
                       from the base case: -0.0353                                                 (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.4449 kcal/mol, Difference in average    
                       score from the base case: -0.0311                                           (00:19:30)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.4758 kcal/mol, Difference in average score  
                       from the base case: -0.0359                                                 (00:19:30)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:39)
Show buried residues
Minimal score value
-4.0922
Maximal score value
2.3383
Average score
-0.8021
Total score value
-352.112
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 Y A -0.9755
2 E A -2.3056
3 H A -1.8021
4 Q A -1.8515
5 T A -0.6960
6 S A -0.6812
7 I A 0.0000
8 P A -0.4774
9 N A -0.4032
10 T A -0.2089
11 V A -0.0147
12 G A -0.2501
13 V A -0.0599
14 P A -0.5479
15 Y A -0.4898
16 K A -0.6479
17 T A -0.1110
18 L A 0.1835
19 V A 0.0000
20 N A -1.1269
21 R A -0.9526
22 P A -0.8531
23 G A -0.4675
24 Y A -0.4047
25 S A -0.2986
26 P A -0.1567
27 M A -0.1906
28 V A -0.1537
29 L A 0.0000
30 E A -0.4849
31 M A 0.0000
32 E A -0.7851
33 L A 0.0000
34 Q A -0.9820
35 S A -0.4940
36 V A 0.0809
37 T A -0.2804
38 L A -0.4666
39 E A -1.3476
40 P A -0.9756
41 T A -0.5978
42 L A -0.1028
43 S A 0.0701
44 L A 0.4292
45 D A -0.3068
46 Y A 0.0000
47 I A 0.0000
48 T A 0.0000
49 C A 0.0000
50 E A -1.9040
51 Y A -1.7716
52 K A -2.3135
53 T A -0.7100
54 V A 0.1586
55 I A 0.8707
56 P A 0.2645
57 S A 0.1393
58 P A 0.4346
59 Y A 1.0567
60 V A 0.7691
61 K A -0.2878
62 C A -0.1752
63 C A -0.1324
64 G A -0.4066
65 T A -0.6595
66 A A -0.7531
67 E A -2.0453
68 C A -2.1058
69 K A -3.1188
70 D A -3.1150
71 K A -2.4718
72 S A -0.9527
73 L A -0.2924
74 P A -0.6002
75 D A -0.9091
76 Y A -0.6701
77 S A -0.8172
78 C A -1.2959
79 K A -1.3513
80 V A -0.2498
81 F A -0.4729
82 T A -1.1791
83 K A -2.4118
84 V A 0.0000
85 S A -0.4796
86 P A 0.0000
87 F A 2.3383
88 M A 1.9110
89 W A 1.5800
90 G A 0.4972
91 G A 0.6578
92 A A 0.9055
93 S A 0.8133
94 C A 0.7635
95 Y A 1.0821
96 C A -0.2426
97 D A -1.8837
98 A A -1.8462
99 E A -2.4887
100 N A 0.0000
101 T A 0.0000
102 Q A 0.0000
103 L A 0.0559
104 S A -0.3827
105 E A -0.5102
106 A A 0.0000
107 H A -0.3784
108 V A 0.0000
109 E A -2.1962
110 K A -2.2976
111 S A -2.3512
112 E A -2.9245
113 S A -1.9489
114 C A 0.0000
115 K A -2.4878
116 T A -1.3926
117 E A -1.5127
118 F A -0.3747
119 A A 0.0000
120 S A 0.0000
121 A A 0.0000
122 Y A -0.2249
123 R A -1.7450
124 A A -1.7568
125 H A -1.8188
126 T A -0.6783
127 A A -0.7167
128 S A -0.4836
129 A A -0.1126
130 S A -0.2106
131 A A -0.4570
132 K A -1.5847
133 L A 0.0000
134 R A -1.5344
135 V A 0.0000
136 L A -0.9419
137 Y A 0.0000
138 Q A -1.7162
139 G A -1.8492
140 N A -1.9360
141 N A -1.8946
142 I A -0.8832
143 T A -0.9069
144 V A 0.0000
145 K A -1.8025
146 A A -0.7181
147 Y A 0.0806
148 A A 0.0000
149 N A -1.5931
150 G A -1.7091
151 D A -2.2126
152 H A -1.2987
153 A A -0.7170
154 V A -0.3492
155 T A -1.2046
156 V A -1.2378
157 K A -2.5324
158 D A -2.9133
159 A A 0.0000
160 K A -2.0627
161 F A 0.0000
162 V A -0.5466
163 V A -0.3114
164 G A -0.7537
165 P A -0.8355
166 M A -0.3986
167 S A -0.4330
168 S A -0.1927
169 A A 0.1678
170 W A 0.3785
171 T A -0.1450
172 P A -0.0158
173 F A -1.5168
174 D A -3.2171
175 N A -3.1737
176 K A -2.7215
177 I A 0.0000
178 V A 0.0000
179 V A -0.2674
180 Y A -0.7086
181 K A -1.9598
182 G A -1.3988
183 D A -0.8574
184 V A 0.0000
185 Y A 0.0000
186 N A -2.1564
187 M A -1.7911
188 D A -2.4830
189 Y A 0.0000
190 P A -0.6807
191 P A -0.3071
192 F A 0.0935
193 G A -0.4285
194 A A -0.5604
195 G A 0.0000
196 R A -2.4368
197 P A -1.8587
198 G A -1.4093
199 Q A -1.6226
200 F A -0.6331
201 G A 0.0000
202 D A 0.0000
203 I A 0.0000
204 Q A 0.0000
205 S A 0.0000
206 R A -2.3917
207 T A -1.8987
208 P A -1.9502
209 E A -2.9804
210 S A -2.7250
211 K A -3.3476
212 D A -3.0881
213 V A -1.4306
214 Y A -0.5610
215 A A -0.8746
216 N A -1.5667
217 T A 0.0000
218 Q A -1.2237
219 L A -0.0004
220 V A 0.8980
221 L A 0.0000
222 Q A -1.3515
223 R A -2.2014
224 P A -0.9353
225 A A -0.4991
226 A A -0.1450
227 G A 0.5332
228 T A 0.6568
229 V A 1.0346
230 H A -0.3505
231 V A -0.1340
232 P A -0.0918
233 Y A 0.5954
234 S A 0.1745
235 Q A -0.2468
236 A A -0.7816
237 P A -0.6919
238 S A 0.0000
239 G A 0.0000
240 F A 0.0000
241 K A -1.2899
242 Y A -0.7581
243 W A -1.2905
244 L A -1.3864
245 K A -2.6783
246 E A -3.0590
247 R A -2.3563
248 G A -1.6656
249 A A -0.9267
250 S A 0.0000
251 L A -0.7617
252 Q A -1.2949
253 H A -1.4018
254 T A -0.6257
255 A A -0.2872
256 P A 0.2704
257 F A 1.4747
258 G A -0.1006
259 C A 0.0000
260 Q A -1.3163
261 I A -0.8654
262 A A -0.7908
263 T A -1.1720
264 N A -1.7405
265 P A -1.3815
266 V A 0.0000
267 R A -1.1361
268 A A 0.0000
269 V A -0.3989
270 N A -0.3104
271 C A 0.3212
272 A A 0.4424
273 V A 0.3515
274 G A -0.5826
275 N A -0.9658
276 I A 0.0000
277 P A -0.6263
278 I A 0.0000
279 S A -1.2562
280 I A -1.3898
281 D A -2.5523
282 I A 0.0000
283 P A -1.6981
284 D A -1.7129
285 A A -0.7604
286 A A -0.6161
287 F A -0.6305
288 T A -0.7666
289 R A -1.0302
290 V A 0.9289
291 V A 1.0768
292 D A -1.0928
293 A A -0.9420
294 P A -1.3017
295 S A -0.7609
296 V A -0.9444
297 T A -0.9951
298 D A -1.9575
299 M A -1.4228
300 S A -1.3412
301 C A -0.9852
302 E A -1.7477
303 V A -0.4480
304 P A -0.3544
305 A A -0.1903
306 C A -0.1367
307 T A -0.6689
308 H A -0.8299
309 S A -1.3103
310 S A -0.6223
311 D A -1.4275
312 F A -0.7359
313 G A -0.3925
314 G A 0.0236
315 V A 0.1192
316 A A 0.0000
317 I A -0.8786
318 I A 0.0000
319 K A -2.3944
320 Y A 0.0000
321 T A -2.0431
322 A A -2.0496
323 S A -1.8340
324 K A -3.2969
325 K A -3.8507
326 G A -2.9331
327 K A -3.4939
328 C A 0.0000
329 A A -1.2833
330 V A 0.0000
331 H A -0.8938
332 S A -0.6296
333 M A -0.4663
334 T A -1.0091
335 N A -1.2536
336 A A -0.7417
337 V A 0.0000
338 T A -0.8858
339 I A 0.0000
340 R A -2.6111
341 E A -2.6384
342 A A -1.8562
343 D A -2.9518
344 V A -2.3484
345 E A -3.4094
346 V A 0.0000
347 E A -4.0922
348 G A -2.6400
349 N A -2.4432
350 S A -2.1117
351 Q A -2.3180
352 L A -1.3711
353 Q A -1.3385
354 I A 0.0000
355 S A -0.6762
356 K A 0.0000
357 S A 0.0000
358 T A 0.0000
359 A A -0.1552
360 L A 0.0000
361 A A -0.3502
362 S A -0.5485
363 A A 0.0000
364 E A -2.2385
365 F A 0.0000
366 R A -2.0875
367 V A 0.0000
368 Q A -0.9175
369 Q A 0.0000
370 C A -0.6302
371 S A -0.2852
372 T A -0.6877
373 Q A -1.2232
374 V A -1.1926
375 H A -1.9457
376 C A 0.0000
377 A A -1.2387
378 A A -0.5489
379 A A -0.3939
380 C A 0.0000
381 H A -1.1778
382 P A -1.4255
383 P A -2.0151
384 K A -2.7202
385 D A -2.3762
386 H A -1.0290
387 I A 1.3682
388 V A 1.4091
389 N A 0.2166
390 Y A 0.5370
391 P A -0.1158
392 A A -0.2670
393 S A -0.3918
394 H A -0.6210
395 T A -0.3288
396 T A 0.0224
397 L A 0.6530
398 G A 0.3400
399 V A 1.0797
400 Q A -0.4380
401 D A -0.3967
402 I A 1.0187
403 S A 0.3909
404 T A 0.4717
405 T A 0.7304
406 A A 1.1308
407 M A 1.0370
408 S A 0.5971
409 W A 1.3198
410 V A 1.1626
411 Q A -0.6631
412 K A -0.7047
413 I A 1.0923
414 T A 0.2073
415 G A -0.8938
416 G A -0.8066
417 V A 0.2543
418 G A -1.3664
419 K A -3.1419
420 Q A -3.2213
421 Q A -3.4417
422 A A -2.9853
423 K A -4.0656
424 D A -3.8793
425 A A -2.8131
426 E A -2.9871
427 I A -0.8091
428 Q A -1.9531
429 N A -2.1292
430 S A -1.1729
431 S A -0.6864
432 L A -0.0076
433 S A -0.8711
434 Q A -1.5912
435 S A -0.8781
436 Y A 0.0839
437 S A -1.1069
438 R A -2.3889
439 H A -1.7602
Download PDB file
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
MR88A -0.7653 -0.0299 View CSV PDB
MK88A -1.0139 -0.0247 View CSV PDB
IK387A -0.5554 -0.0353 View CSV PDB
IR387A -0.4758 -0.0359 View CSV PDB
VK388A -0.6089 -0.0304 View CSV PDB
FR87A -0.2424 -0.0446 View CSV PDB
FK87A -0.0161 -0.0444 View CSV PDB
VR388A -0.194 -0.0304 View CSV PDB
WK89A -0.0424 -0.0237 View CSV PDB
WE89A -0.0129 -0.0247 View CSV PDB
FK257A 0.8356 -0.0342 View CSV PDB
FR257A 1.2516 -0.0418 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018